English Premier League side Swansea secured a last 32 berth in the Europa League despite losing 1-0 to FC Gallen in Switzerland.
The Welsh club finished second in Group A, behind winners Valencia of Spain, who held third-placed Kuban Krasnodar of Russia to a 1-1 draw.
Ludogorets were already guaranteed of finishing the preliminary rounds as Group B winners ahead of the final round of matches but finished off with a 2-1 win at Dinamo Zagreb.
Dutch side PSV Eindhoven failed to progress into the next round following their 1-0 at home to Ukrainians FC Chornomorets Odesa, who clinched the group’s second spot at the expense of the hosts.
In Group C Salzburg went into Thursday’s last group match guaranteed of the top spot but the Austrians ensured they completed the stage with a flawless record by beating Esbjerg of Denmark 3-0.
Esbjerg had already clinched the second place making Swedish side Elfsborg’s 3-1 win at Standard Liege of Belgium irrelevant.
Group D winners Rubin Kazan of Russia beat Belgium side Zulte Weregem 2-0.
Following the ouster of Owen Coyle, new Wigan coach Uwe Rosler ended his first game in charge of the Latics in defeat. The last season’s FA Cup winners lost 2-1 to Slovenians Maribor at the Ljudski Vrt.
A win would have sent Wigan through as Maribor started the day bottom of the group standings. Maribor’s coupled with Rubin’s win over Zulte ensured they finished second.
Italians Fiorentina won Group E with a 2-1 win over Ukraine’s Dnipro Dnipropetrovsk, who finished second.
Maccabi Tel Aviv made sure of second in Group F by beating French side Bordeaux 1-0. Group winners Eintracht Frankfurt of Germany beat Cyprus side APOEL Nicosia 2-0.
Dynamo Kiev of Ukraine eventually claimed the runners-up position oof Group G after beating Ausrians SK Rapid Vienna 3-1. Belgian side Genk, who had already won the group, edged FC Thun of Switzerland 1-0.
Spaniards Sevilla cemented top spot in Group H after beating FC Freiburg 2-0 in Germany. Czech side Slovan Liberec came second with a 2-1 win at Estoril of Portugal.
French club Lyon and Betis progressed into the round of 32 from Group I. Lyon finished top by coming from behind to beat Portuguese side Vitoria Guimaraes 2-1, while Spanish side Betis drew goalless with Croatians HNK Rikeka.
Italians Lazio and Turkish club Trabzonspor go through from Group J after both sides played out a 0-0 draw. Trabzonspor won the group and Lazio finished as runners-up.
Group K winners Tottenham completed six wins from six with a 4-1 victory against Russian side Anzhi Makhachkala, who finished second.
The draw for the round of 32 takes place on Monday at 12:00 GMT, with the first and second leg fixtures played on the 20 and 27 February next year.